The parameters described below can be specified when the pipeline is run. They change the behavior of various stages.
A local directory in which to write the final output files, including the
aggregated results and error reports. A reasonable choice would be
Protein Receptor (Pocket)¶
The values below describe the protein receptor we will “grow” molecules for in the denovo step.
Description of the protein receptor, in PDB format.
X coordinate of the pocket center
Y coordinate of the pocket center
Z coordinate of the pocket center
size in the X dimension (Angstroms)
size in the Y dimension (Angstroms)
size in the Z dimension (Angstroms)
Denovo (Stage 3)¶
A SMILES file (.smi) containing one or more SMILES strings for molecules to use in place of building denovo ligands with Autogrow4. This causes Stage 3 to be skipped, the ligands specified will be fed directly into Stage 4.
The value to use for the
docking_exhaustiveness parameter to Autogrow4. The
default is 1.
The number of generations to produce with Autogrow4. Drug Sniffer uses the last three generations, so this value must be at least 3. The default is 20.
Similarity Search (Stage 4)¶
The path to the molecule database to use.
The minimum Tanimoto coefficient to consider two molecules a match.
ADMET Prediction (Stage 7)¶
A space-separated list of ADMET checks to perform, see the FPADMET documentation for a list of available checks.